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Structure of a B-DNA Dodecamer: Conformation and Dynamics

Drew, Horace R. and Wing, Richard M. and Takano, Tsunehiro and Broka, Christopher and Tanaka, Shoji and Itakura, Keiichi and Dickerson, Richard E. (1981) Structure of a B-DNA Dodecamer: Conformation and Dynamics. Proceedings of the National Academy of Sciences of the United States of America, 78 (4). pp. 2179-2183. ISSN 0027-8424. http://resolver.caltech.edu/CaltechAUTHORS:DREpnas81

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Abstract

The crystal structure of the synthetic DNA dodecamer d(CpGpCpGpApApTpTpCpGpCpG) has been refined to a residual error of R = 17.8% at 1.9-angstrom resolution (two-sigma data). The molecule forms slightly more than one complete turn of righthanded double-stranded B helix. The two ends of the helix overlap and interlock minor grooves with neighboring molecules up and down a 21 screw axis, producing a 19 degrees bend in helix axis over the 11-base-pair steps of the dodecamer. In the center of the molecule, where perturbation is least, the helix has a mean rotation of 36.9 degrees per step, or 9.8 base pairs per turn. The mean propeller twist (total dihedral angle between base planes) between A·T base pairs in the center of the molecule is 17.3 degrees, and that between C· G pairs on the two ends averages 11.5 degrees. Individual deoxyribose ring conformations as measured by the C5'-C4'-C3'-O3' torsion angle delta , exhibit an approximately Gaussian distribution centered around the C1'-exo position with delta avg=123 degrees and a range of 79 degrees to 157 degrees. Purine sugars cluster at high delta values, and pyrimidine sugars cluster at lower delta . A tendency toward 2-fold symmetry in sugar conformation about the center of the molecule is detectable in spite of the destruction of ideal 2-fold symmetry by the molecular bending. More strikingly, sugar conformations of paired bases appear to follow a "principle of anticorrelation," with delta values lying approximately the same distance to either side of the center value, delta =123 degrees. This same anticorrelation is also observed in other DNA and DNA· RNA structures.


Item Type:Article
Additional Information:Copyright © 1981 by the National Academy of Sciences Communicated by P. D. Boyer, December 31, 1980 We thank Peter Dembek for his help in synthesis of the dodecamer and Lillian Casler for her assistance in preparing the figures. This work was carried out with the support of National Institutes of Health Grants GM-12121 and GM-24393 and National Science Foundation Grant PCM79-13959. H.R.D. was the recipient of a National Institutes of Health Predoctoral Traineeship. This is contribution no. 6317 from the Division of Chemistry and Chemical Engineering. This is paper no. 1 of a series; paper no. 2 is ref. 1. The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact.
Subject Keywords:DNA structure; sugar puckering in DNA; principle of anticorrelation; torsion angles in DNA; thermal vibration in DNA
Record Number:CaltechAUTHORS:DREpnas81
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:DREpnas81
Alternative URL:http://www.pnas.org/cgi/content/abstract/78/4/2179
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:5825
Collection:CaltechAUTHORS
Deposited By: Archive Administrator
Deposited On:03 Nov 2006
Last Modified:14 Nov 2014 19:19

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